Freshwater algal blooms are the result of an excess of nutrients, particularly some phosphates. The excess of nutrients may originate from fertilizers that are applied to land for agricultural or recreational purposes. They may also originate from household cleaning products containing phosphorus. These nutrients can then enter watersheds through water runoff. When phosphates are introduced into water systems, higher concentrations cause increased growth of algae and plants. Algae tend to grow very quickly under high nutrient availability, but each alga is short-lived, and the result is a high concentration of dead organic matter which starts to decay. The decay process consumes dissolved oxygen in the water, resulting in hypoxic conditions. Without sufficient dissolved oxygen in the water, animals and plants may die in large numbers.

A harmful algal bloom (HAB) is an algal bloom that causes negative impacts to other organisms via production of natural toxins, mechanical damage to other organisms. It is unclear what causes a HAB; their occurrence in some locations appears to be entirely natural, while in others they appear to be a result of human activities. Furthermore, there are many different species of algae that can form HABs, each with different environmental requirements for optimal growth. The frequency and severity of HABs in some parts of the world have been linked to increased nutrient loading from human activities. In other areas, HABs are a predictable seasonal occurrence resulting from coastal upwelling. The growth of marine phytoplankton (both non-toxic and toxic) is generally limited by the availability of nitrates and phosphates, which can be abundant in coastal upwelling zones as well as in agricultural run-off. The type of nitrates and phosphates available in the system are also a factor, since phytoplankton can grow at different rates depending on the relative abundance of these substances (e.g. ammonia, urea, nitrate ion). A variety of other nutrient sources can also play an important role in affecting algal bloom formation, including iron, silica or carbon.